[CP2K-user] errors when calculate the electron density data with cp2k
董济超
dj... at outlook.com
Sat Aug 3 09:06:12 UTC 2019
Dear all,
When I finished AIMD simulations, I want to calculate the electron density
data from the md trajectory.
However, there is an error appears as follows in the "log" file:
********************************************
*** ERROR in open_file (MODULE cp_files) ***
********************************************
*** Attempt to re-open the existing file <PropOx-pos-1.xyz> with the
***
*** modified ACTION attribute WRITE. The current ACTION attribute is READ.
***
*** Program stopped at line number 396 of MODULE cp_files ***
===== Routine Calling Stack =====
5 write_trajectory
4 md_write_output
3 md_output
2 qs_mol_dyn_low
1 CP2K
Could anyone know how to fix this problem?
If you know how,please show me. It would be very helpful and thank you very
much!
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DBCSR| Multiplication driver SMM
DBCSR| Multrec recursion limit 512
DBCSR| Multiplication stack size 1000
DBCSR| Multiplication size stacks 3
DBCSR| Use subcommunicators T
DBCSR| Use MPI combined types F
DBCSR| Use MPI memory allocation T
DBCSR| Use Communication thread T
DBCSR| Communication thread load 87
**** **** ****** ** PROGRAM STARTED AT 2019-08-03 16:19:38.493
***** ** *** *** ** PROGRAM STARTED ON cn990
** **** ****** PROGRAM STARTED BY
***** ** ** ** ** PROGRAM PROCESS ID 27863
**** ** ******* ** PROGRAM STARTED IN /vol-th/home/lmxu/DongJichao/IRspectr
a_test1/electron-density/IR/block1
CP2K| version string: CP2K version 2.5.0
CP2K| source code revision number: svn:13632
CP2K| is freely available from http://www.cp2k.org/
CP2K| Program compiled at Mon Sep 14 11:18:07 CST 2015
CP2K| Program compiled on ln1
CP2K| Program compiled for Linux-x86-64-intel
CP2K| Input file name input.inp
GLOBAL| Force Environment number 1
GLOBAL| Basis set file name BASIS_MOLOPT
GLOBAL| Geminal file name BASIS_GEMINAL
GLOBAL| Potential file name POTENTIAL
GLOBAL| MM Potential file name MM_POTENTIAL
GLOBAL| Coordinate file name __STD_INPUT__
GLOBAL| Method name CP2K
GLOBAL| Project name PropOx
GLOBAL| Preferred FFT library FFTW3
GLOBAL| Preferred diagonalization lib. SL
GLOBAL| Run type MD
GLOBAL| All-to-all communication in single precision F
GLOBAL| FFTs using library dependent lengths F
GLOBAL| Global print level LOW
GLOBAL| Total number of message passing processes 36
GLOBAL| Number of threads for this process 1
GLOBAL| This output is from process 0
MEMORY| system memory details [Kb]
MEMORY| rank 0 min max average
MEMORY| MemTotal 24729928 24729928 24729928 24729928
MEMORY| MemFree 21043364 21043364 22224776 21732982
MEMORY| Buffers 0 0 0 0
MEMORY| Cached 1655908 587620 1655908 1026338
MEMORY| Slab 581468 459516 581468 515048
MEMORY| SReclaimable 18212 14956 18212 16548
MEMORY| MemLikelyFree 22717484 22717484 22827352 22775869
GENERATE| Preliminary Number of Bonds generated: 0
GENERATE| Achieved consistency in connectivity generation.
*******************************************************************************
*******************************************************************************
** **
** ##### ## ## **
** ## ## ## ## ## **
** ## ## ## ###### **
** ## ## ## ## ## ##### ## ## #### ## ##### ##### **
** ## ## ## ## ## ## ## ## ## ## ## ## ## ## **
** ## ## ## ## ## ## ## #### ### ## ###### ###### **
** ## ### ## ## ## ## ## ## ## ## ## ## **
** ####### ##### ## ##### ## ## #### ## ##### ## **
** ## ## **
** **
** ... make the atoms dance **
** **
** Copyright (C) by CP2K Developers Group (2000 - 2014) **
** **
*******************************************************************************
SCF PARAMETERS Density guess: ATOMIC
--------------------------------------------------------
max_scf: 15
max_scf_history: 0
max_diis: 4
--------------------------------------------------------
eps_scf: 1.00E-06
eps_scf_history: 0.00E+00
eps_diis: 1.00E-01
eps_eigval: 1.00E-05
--------------------------------------------------------
level_shift [a.u.]: 0.00
--------------------------------------------------------
Outer loop SCF in use
No variables optimised in outer loop
eps_scf 1.00E-06
max_scf 20
No outer loop optimization
step_size 5.00E-01
MD| Molecular Dynamics Protocol
MD| Ensemble Type REFTRAJ
MD| Number of Time Steps 2000
MD| Time Step [fs] 0.50
MD| Temperature [K] 300.00
MD| Temperature tolerance [K] 0.00
MD| Print MD information every 1 step(s)
MD| File type Print frequency[steps] File names
MD| Coordinates 1 PropOx-pos-1.xyz
MD| Velocities 1 PropOx-vel-1.xyz
MD| Energies 1 PropOx-1.ener
MD| Dump 0 PropOx-1.restart
ROT| Rotational Analysis Info
ROT| Principal axes and moments of inertia in atomic units:
ROT| 1 2 3
ROT| EIGENVALUES 0.453667631E+09 0.493138757E+09 0.555250371E+09
ROT| X 0.691757071 -0.179230919 -0.699534440
ROT| Y 0.717011669 0.055340669 0.694860904
ROT| Z -0.085827855 -0.982249300 0.166792960
ROT| Numer of Rotovibrational vectors: 6
Calculation of degrees of freedom
Number of atoms: 320
Number of Intramolecular constraints: 0
Number of Intermolecular constraints: 0
Invariants(translation + rotations): 3
Degrees of freedom: 957
Restraints Information
Number of Intramolecular restraints: 0
Number of Intermolecular restraints: 0
************************** Velocities initialization **************************
Initial Temperature 300.00 K
COM velocity: 0.000000000000 0.000000000000 -0.000000000000
*******************************************************************************
Number of electrons: 768
Number of occupied orbitals: 384
Number of molecular orbitals: 384
Number of orbital functions: 2624
Number of independent orbital functions: 2624
Extrapolation method: initial_guess
SCF WAVEFUNCTION OPTIMIZATION
----------------------------------- OT ---------------------------------------
Allowing for rotations: F
Optimizing orbital energies: F
Minimizer : DIIS : direct inversion
in the iterative subspace
using : - 7 DIIS vectors
- safer DIIS on
Preconditioner : FULL_KINETIC : cholesky inversion of T + eS
Precond_solver : DEFAULT
stepsize : 0.15000000
energy_gap : 0.20000000
eps_taylor : 0.10000E-15
max_taylor : 4
mixed_precision : F
----------------------------------- OT ---------------------------------------
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 OT DIIS 0.15E+00 4.0 0.01307166 -1094.9305635163 -1.09E+03
2 OT DIIS 0.15E+00 2.2 0.00919471 -1116.0853042428 -2.12E+01
3 OT DIIS 0.15E+00 2.2 0.00663192 -1133.4980870709 -1.74E+01
4 OT DIIS 0.15E+00 2.2 0.00504823 -1143.8271742615 -1.03E+01
5 OT DIIS 0.15E+00 2.2 0.00382448 -1151.0803321035 -7.25E+00
6 OT DIIS 0.15E+00 2.2 0.00290074 -1156.3735282406 -5.29E+00
7 OT DIIS 0.15E+00 2.4 0.00211944 -1160.1871601348 -3.81E+00
8 OT DIIS 0.15E+00 2.2 0.00174506 -1161.9684852770 -1.78E+00
9 OT DIIS 0.15E+00 2.2 0.00132578 -1163.4315307191 -1.46E+00
10 OT DIIS 0.15E+00 2.2 0.00116494 -1164.0808171298 -6.49E-01
11 OT DIIS 0.15E+00 2.2 0.00093083 -1164.7759005280 -6.95E-01
12 OT DIIS 0.15E+00 2.2 0.00073259 -1165.2811271092 -5.05E-01
13 OT DIIS 0.15E+00 2.2 0.00063104 -1165.5924357753 -3.11E-01
14 OT DIIS 0.15E+00 2.2 0.00053463 -1165.8150511352 -2.23E-01
15 OT DIIS 0.15E+00 2.2 0.00048871 -1165.9879656507 -1.73E-01
*** SCF run NOT converged ***
Electronic density on regular grids: -767.9999999833 0.0000000167
Core density on regular grids: 767.9999999995 -0.0000000005
Total charge density on r-space grids: 0.0000000162
Total charge density g-space grids: 0.0000000162
Overlap energy of the core charge distribution: 0.00006269395543
Self energy of the core charge distribution: -2887.53533513526327
Core Hamiltonian energy: 875.43057234485059
Hartree energy: 1188.48678002032784
Exchange-correlation energy: -342.37004557458084
Total energy: -1165.98796565071029
outer SCF iter = 1 RMS gradient = 0.49E-03 energy = -1165.9879656507
----------------------------------- OT ---------------------------------------
Allowing for rotations: F
Optimizing orbital energies: F
Minimizer : DIIS : direct inversion
in the iterative subspace
using : - 7 DIIS vectors
- safer DIIS on
Preconditioner : FULL_KINETIC : cholesky inversion of T + eS
Precond_solver : DEFAULT
stepsize : 0.15000000
energy_gap : 0.20000000
eps_taylor : 0.10000E-15
max_taylor : 4
mixed_precision : F
----------------------------------- OT ---------------------------------------
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 OT DIIS 0.15E+00 4.8 0.00062683 -1166.1252547620 -1.37E-01
2 OT DIIS 0.15E+00 2.2 0.00057386 -1166.1819047431 -5.66E-02
3 OT DIIS 0.15E+00 2.2 0.00045694 -1166.3471459669 -1.65E-01
4 OT DIIS 0.15E+00 2.3 0.00035506 -1166.4977859607 -1.51E-01
5 OT DIIS 0.15E+00 2.3 0.00023131 -1166.6166848645 -1.19E-01
6 OT DIIS 0.15E+00 2.2 0.00021453 -1166.6203232213 -3.64E-03
7 OT DIIS 0.15E+00 2.2 0.00012652 -1166.6632523423 -4.29E-02
8 OT DIIS 0.15E+00 2.2 0.00008497 -1166.6740400624 -1.08E-02
9 OT DIIS 0.15E+00 2.2 0.00006116 -1166.6785242467 -4.48E-03
10 OT DIIS 0.15E+00 2.2 0.00004427 -1166.6808755001 -2.35E-03
11 OT DIIS 0.15E+00 2.2 0.00002768 -1166.6824029775 -1.53E-03
12 OT DIIS 0.15E+00 2.2 0.00002013 -1166.6827889399 -3.86E-04
13 OT DIIS 0.15E+00 2.2 0.00001603 -1166.6829701624 -1.81E-04
14 OT DIIS 0.15E+00 2.2 0.00001049 -1166.6831572472 -1.87E-04
15 OT DIIS 0.15E+00 2.2 0.00000710 -1166.6832284557 -7.12E-05
*** SCF run NOT converged ***
Electronic density on regular grids: -767.9999999838 0.0000000162
Core density on regular grids: 767.9999999995 -0.0000000005
Total charge density on r-space grids: 0.0000000157
Total charge density g-space grids: 0.0000000157
Overlap energy of the core charge distribution: 0.00006269395543
Self energy of the core charge distribution: -2887.53533513526327
Core Hamiltonian energy: 876.04834033015516
Hartree energy: 1187.53798515043331
Exchange-correlation energy: -342.73428149497943
Total energy: -1166.68322845569901
outer SCF iter = 2 RMS gradient = 0.71E-05 energy = -1166.6832284557
----------------------------------- OT ---------------------------------------
Allowing for rotations: F
Optimizing orbital energies: F
Minimizer : DIIS : direct inversion
in the iterative subspace
using : - 7 DIIS vectors
- safer DIIS on
Preconditioner : FULL_KINETIC : cholesky inversion of T + eS
Precond_solver : DEFAULT
stepsize : 0.15000000
energy_gap : 0.20000000
eps_taylor : 0.10000E-15
max_taylor : 4
mixed_precision : F
----------------------------------- OT ---------------------------------------
Step Update method Time Convergence Total energy Change
------------------------------------------------------------------------------
1 OT DIIS 0.15E+00 4.9 0.00000621 -1166.6832546208 -2.62E-05
2 OT DIIS 0.15E+00 2.1 0.00000554 -1166.6832601153 -5.49E-06
3 OT DIIS 0.15E+00 2.2 0.00000342 -1166.6832786120 -1.85E-05
4 OT DIIS 0.15E+00 2.1 0.00000230 -1166.6832870240 -8.41E-06
5 OT DIIS 0.15E+00 2.1 0.00000137 -1166.6832915997 -4.58E-06
6 OT DIIS 0.15E+00 2.1 0.00000072 -1166.6832931535 -1.55E-06
*** SCF run converged in 6 steps ***
Electronic density on regular grids: -767.9999999838 0.0000000162
Core density on regular grids: 767.9999999995 -0.0000000005
Total charge density on r-space grids: 0.0000000157
Total charge density g-space grids: 0.0000000157
Overlap energy of the core charge distribution: 0.00006269395543
Self energy of the core charge distribution: -2887.53533513526327
Core Hamiltonian energy: 876.05214352933501
Hartree energy: 1187.53476613630187
Exchange-correlation energy: -342.73493037785227
Total energy: -1166.68329315352321
outer SCF iter = 3 RMS gradient = 0.72E-06 energy = -1166.6832931535
outer SCF loop converged in 3 iterations or 36 steps
The electron density is written in cube file format to the file:
/vol-th/home/lmxu/DongJichao/IRspectra_test1/electron-density/IR/block1/result.cube
ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.): -1166.683293480909924
MD_ENERGIES| Initialization proceeding
******************************** GO CP2K GO! **********************************
INITIAL POTENTIAL ENERGY[hartree] = -0.116668329348E+04
INITIAL VOLUME[bohr^3] = 0.255382787390E+05
INITIAL CELL LNTHS[bohr] = 0.2944855E+02 0.2944855E+02 0.2944855E+02
INITIAL CELL ANGLS[deg] = 0.9000000E+02 0.9000000E+02 0.9000000E+02
******************************** GO CP2K GO! **********************************
********************************************
*** ERROR in open_file (MODULE cp_files) ***
********************************************
*** Attempt to re-open the existing file <PropOx-pos-1.xyz> with the ***
*** modified ACTION attribute WRITE. The current ACTION attribute is READ. ***
*** Program stopped at line number 396 of MODULE cp_files ***
===== Routine Calling Stack =====
5 write_trajectory
4 md_write_output
3 md_output
2 qs_mol_dyn_low
1 CP2K
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